Contacts of the helix formed by residues 20 - 37 (chain Q) in PDB entry 2LPZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 20 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L ALA 3.3 15.5 - - - +
38L PRO* 3.5 26.0 - - + -
16Q PHE* 3.3 29.8 - - + +
17Q ASP* 2.9 6.3 + - - +
19Q GLY* 1.3 81.5 - - - +
21Q ASP* 1.3 63.0 + - - +
22Q ASN 3.1 3.6 - - - +
23Q LEU* 3.1 28.0 + - + +
24Q GLN 3.7 0.2 + - - -
57Q TYR* 3.2 39.4 - - + -
5W TRP* 3.6 14.1 - - + +
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Residues in contact with ASP 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ASP* 2.5 22.5 + - - +
18Q THR* 3.8 12.3 + - - +
19Q GLY 3.7 1.0 - - - -
20Q VAL* 1.3 75.4 - - - +
22Q ASN* 1.3 68.2 + - - +
23Q LEU 3.6 0.2 + - - -
24Q GLN* 3.9 11.6 + - - +
25Q THR* 4.0 10.4 + - - -
57Q TYR* 5.0 6.5 + - - -
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Residues in contact with ASN 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q VAL* 3.1 0.6 - - - +
21Q ASP* 1.3 86.6 - - - +
23Q LEU* 1.3 66.8 + - - +
24Q GLN 3.2 0.7 - - - -
25Q THR* 3.0 10.7 + - - -
26Q GLN* 2.8 35.9 + - + +
3W THR 5.5 1.0 + - - -
4W PRO* 5.3 2.2 - - - +
5W TRP* 3.8 36.5 - - + +
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Residues in contact with LEU 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L PRO* 5.8 1.3 - - + -
20Q VAL* 3.1 29.7 + - + +
22Q ASN* 1.3 77.7 - - - +
24Q GLN* 1.3 64.2 + - - +
26Q GLN* 3.2 4.3 + - - +
27Q VAL* 3.0 21.9 + - + +
50Q LYS* 3.5 30.7 - - + +
53Q GLU* 3.7 31.9 - - + +
54Q TYR* 4.2 5.8 - - + +
57Q TYR* 3.8 23.8 - - + -
5W TRP* 3.7 36.7 - - + -
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Residues in contact with GLN 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ALA* 5.4 4.6 - - - +
20Q VAL 3.7 2.0 + - - -
21Q ASP* 4.2 7.9 - - - +
22Q ASN 3.2 0.2 - - - -
23Q LEU* 1.3 79.5 - - - +
25Q THR* 1.3 55.7 + - - +
27Q VAL* 3.3 8.3 - - - +
28Q THR* 2.7 44.6 + - - +
54Q TYR* 4.0 17.4 + - + +
57Q TYR* 2.8 33.9 + - + +
58Q ARG* 3.6 22.6 + - - +
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Residues in contact with THR 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASP 4.0 8.5 + - - -
22Q ASN* 3.0 14.4 + - - -
24Q GLN* 1.3 80.2 - - - +
26Q GLN* 1.3 59.8 + - + +
28Q THR* 3.4 5.0 + - - -
29Q GLU* 3.0 52.0 + - + +
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Residues in contact with GLN 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q ASN* 2.8 25.7 + - + +
23Q LEU* 3.6 3.5 - - - +
25Q THR* 1.3 78.3 - - + +
27Q VAL* 1.3 57.6 + - - +
29Q GLU* 3.4 8.5 + - - +
30Q ALA* 2.9 28.1 + - - +
50Q LYS* 2.9 40.5 + - + +
4W PRO* 4.4 8.7 - - - +
5W TRP* 3.0 58.2 + - - +
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Residues in contact with VAL 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q LEU 3.0 13.9 + - - +
24Q GLN 3.3 11.4 - - - +
26Q GLN* 1.3 75.5 - - - +
28Q THR* 1.3 67.7 + - - +
30Q ALA* 4.0 4.3 - - - -
31Q LEU* 3.0 21.8 + - - +
47Q TYR* 3.4 30.4 - - + +
50Q LYS* 3.8 13.0 - - + +
51Q LEU* 3.7 36.8 - - + +
54Q TYR* 3.8 28.5 - - + -
68V PHE* 6.1 3.9 - - + -
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Residues in contact with THR 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q GLN* 2.7 32.6 + - - +
25Q THR* 3.7 6.9 - - - -
27Q VAL* 1.3 77.6 - - - +
29Q GLU* 1.3 62.4 + - + +
31Q LEU* 3.2 10.9 + - + +
32Q ASP* 2.9 40.4 + - - +
54Q TYR* 5.8 0.5 - - - -
68V PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q THR* 3.0 37.9 + - + +
26Q GLN* 3.8 7.8 - - - +
28Q THR* 1.3 75.3 - - + +
30Q ALA* 1.3 60.9 + - - +
32Q ASP* 3.3 13.6 + - - +
33Q LYS* 3.0 45.8 + - - +
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Residues in contact with ALA 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q GLN 2.9 18.1 + - - +
27Q VAL* 3.7 8.3 - - - +
29Q GLU* 1.3 78.6 - - - +
31Q LEU* 1.3 56.2 + - - +
33Q LYS* 4.0 6.6 - - - +
34Q LEU* 2.9 31.4 + - - +
43Q LEU* 4.8 6.3 - - + +
46Q ALA* 4.8 6.1 - - + -
47Q TYR* 3.8 32.8 - - + +
50Q LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q VAL 3.0 15.6 + - - +
28Q THR* 3.4 14.4 - - + +
30Q ALA* 1.3 75.7 - - - +
32Q ASP* 1.3 63.0 + - - +
34Q LEU* 4.3 6.1 - - + -
35Q ALA* 2.8 34.5 + - + +
47Q TYR* 3.6 29.3 - - + +
12V VAL* 5.1 7.4 - - + +
15V LYS* 5.0 22.2 - - + -
16V PHE* 5.3 12.3 - - + +
64V THR* 4.4 14.1 - - + +
68V PHE* 3.8 31.4 - - + -
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Residues in contact with ASP 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q THR* 2.9 31.2 + - - +
29Q GLU* 3.3 17.6 + - - +
31Q LEU* 1.3 82.0 - - - +
33Q LYS* 1.3 63.7 + - + +
35Q ALA* 3.5 14.9 - - - +
36Q ALA* 3.7 6.6 + - - +
15V LYS* 5.3 12.8 + - - +
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Residues in contact with LYS 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q GLU* 3.0 30.9 + - - +
30Q ALA* 4.0 3.6 - - - +
32Q ASP* 1.3 76.8 - - + +
34Q LEU* 1.3 65.0 + - - +
36Q ALA* 2.9 18.7 + - - +
37Q LYS 3.2 8.1 + - - -
43Q LEU* 3.5 32.4 - - + +
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Residues in contact with LEU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ALA 2.9 18.9 + - - +
31Q LEU* 3.7 8.7 - - + +
33Q LYS* 1.3 77.0 - - - +
35Q ALA* 1.3 57.2 - - - +
37Q LYS 3.0 13.0 - - - +
38Q PRO* 2.8 55.5 - - + +
40Q ASP 4.3 0.2 - - - +
43Q LEU* 3.5 30.0 - - + +
44Q LEU* 3.6 24.9 - - + +
47Q TYR* 3.3 38.8 - - + -
16V PHE* 5.4 6.1 - - + -
60V ALA* 6.2 2.2 - - + -
64V THR* 5.4 4.7 - - + -
79b PHE* 5.6 1.6 - - + -
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Residues in contact with ALA 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q LEU* 2.8 19.0 + - + +
32Q ASP* 3.5 10.1 - - - +
33Q LYS 3.1 0.2 - - - -
34Q LEU* 1.3 78.9 - - - +
36Q ALA* 1.3 59.4 + - - +
38Q PRO* 3.6 0.9 - - - +
15V LYS 3.4 26.2 - - - +
16V PHE* 3.6 27.1 - - + +
19V GLY* 3.2 22.8 - - - +
20V VAL* 3.3 12.0 - - - +
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Residues in contact with ALA 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q ASP 3.7 5.3 + - - +
33Q LYS* 2.9 14.7 + - - +
35Q ALA* 1.3 80.0 - - - +
37Q LYS* 1.3 66.1 + - + +
38Q PRO* 3.6 0.4 - - - -
19V GLY* 3.5 14.0 - - - +
5b TRP* 2.7 36.4 + - + +
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Residues in contact with LYS 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q LYS 3.2 3.0 + - - -
34Q LEU* 3.0 12.4 + - - +
36Q ALA* 1.3 89.6 - - + +
38Q PRO* 1.3 67.3 - - - +
39Q SER 3.0 4.1 + - - +
40Q ASP* 3.1 27.4 + - + +
43Q LEU* 3.7 14.7 - - + +
6b SER 3.5 22.7 - - - +
7b GLY* 4.2 1.6 - - - -
8b TYR* 4.0 24.2 - - + +
11b ASP* 2.8 22.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il